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authorRoel Janssen <roel@gnu.org>2017-01-12 10:02:57 +0100
committerRoel Janssen <roel@gnu.org>2017-01-12 10:02:57 +0100
commitc5173d74d67b786c36dd53930c5d4fe4805cf3e9 (patch)
tree4536c52f7d2b8eef6b400a977c685dd70cae342e
parenteefd042e60d9fc1d092b44bf80ecbfe65b291e46 (diff)
gnu: Add r-txdb-mmusculus-ucsc-mm10-knowngene.
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm35
1 files changed, 35 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 14daf59c92..d82b6c093c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7100,6 +7100,41 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
in Biostrings objects.")
(license license:artistic2.0)))
+(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
+ (package
+ (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
+ (version "3.4.0")
+ (source (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/annotation/" instead of "bioc/".
+ (uri (string-append "http://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "TxDb.Mmusculus.UCSC.mm10.knownGene_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
+ (properties
+ `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
+ (build-system r-build-system)
+ ;; As this package provides little more than a very large data file it
+ ;; doesn't make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-annotationdbi" ,r-annotationdbi)))
+ (home-page
+ "http://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
+ (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
+ (description
+ "This package loads a TxDb object, which is an R interface to
+prefabricated databases contained in this package. This package provides
+the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
+based on the knownGene track.")
+ (license license:artistic2.0)))
+
(define-public r-bsgenome-celegans-ucsc-ce6
(package
(name "r-bsgenome-celegans-ucsc-ce6")